Mutagenetix > Incidental Mutation

Incidental Mutation 'R5517:Smg9'

431345

Institutional Source

Beutler Lab

Gene Symbol

Smg9

Ensembl Gene

ENSMUSG00000002210

Gene Name

SMG9 nonsense mediated mRNA decay factor

Synonyms

smg-9 homolog, nonsense mediated mRNA decay factor (C. elegans), 1500002O20Rik, N28092

MMRRC Submission

043076-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5517 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

24099106-24122197 bp(+) (GRCm39)

Type of Mutation

unclassified

DNA Base Change (assembly)

C to A at 24114338 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Gene Model

predicted gene model for transcript(s): [ENSMUST00000002280]

AlphaFold

Q9DB90

Predicted Effect

probably benign
Transcript: ENSMUST00000002280

SMART Domains

Protein: ENSMUSP00000002280
Gene: ENSMUSG00000002210

Domain	Start	End	E-Value	Type
low complexity region	79	93	N/A	INTRINSIC
low complexity region	112	135	N/A	INTRINSIC
Pfam:DUF2146	199	373	3.7e-8	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000123188

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000148288

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 98.5%
3x: 97.4%
10x: 95.2%
20x: 90.5%

Validation Efficiency

99% (67/68)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a regulatory subunit of the SMG1 complex, which plays a critical role in nonsense-mediated mRNA decay (NMD). Binding of the encoded protein to the SMG1 complex kinase scaffold protein results in the inhibition of its kinase activity. Mutations in this gene cause a multiple congenital anomaly syndrome in human patients, characterized by brain malformation, congenital heart disease and other features. [provided by RefSeq, Jul 2016]
PHENOTYPE: Mice homozygous for a severe hypomorphic allele exhibit edema, hemorrhage, exencephaly, preaxial polydactyly, reduced size and growth, decreased mid- and hindrain size, microphthalmia, thin myocardium and atrioventricular septal defect. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 54 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcf1	C	T	17: 36,269,233 (GRCm39)	R675K	possibly damaging	Het
Aire	A	T	10: 77,875,525 (GRCm39)	S282T	probably benign	Het
Ak9	A	G	10: 41,216,887 (GRCm39)	E283G	probably benign	Het
Akap9	T	A	5: 4,051,665 (GRCm39)	D1477E	possibly damaging	Het
Ap2a1	T	C	7: 44,556,405 (GRCm39)	D273G	possibly damaging	Het
Apob	T	C	12: 8,040,906 (GRCm39)	L664P	probably damaging	Het
Arhgap35	A	T	7: 16,297,414 (GRCm39)	F550L	probably damaging	Het
Armc2	T	C	10: 41,839,846 (GRCm39)	E373G	probably benign	Het
Atp8b2	C	A	3: 89,853,338 (GRCm39)	A726S	probably benign	Het
C030048H21Rik	T	A	2: 26,145,899 (GRCm39)	Q87L	probably damaging	Het
Cd244a	T	A	1: 171,405,542 (GRCm39)		probably benign	Het
Cdk10	T	A	8: 123,957,326 (GRCm39)		probably null	Het
Cenpe	C	A	3: 134,929,026 (GRCm39)	P310Q	probably damaging	Het
Chuk	T	A	19: 44,085,972 (GRCm39)		probably null	Het
Crebl2	T	C	6: 134,828,139 (GRCm39)	S104P	probably benign	Het
Ddo	A	G	10: 40,523,726 (GRCm39)	K239E	probably benign	Het
Defb5	A	G	8: 19,300,868 (GRCm39)		probably null	Het
Dhx35	T	A	2: 158,676,832 (GRCm39)	M422K	probably damaging	Het
Fchsd1	C	T	18: 38,092,926 (GRCm39)		probably benign	Het
Gatm	G	A	2: 122,426,024 (GRCm39)	T409I	probably damaging	Het
Gdpd1	A	T	11: 86,950,332 (GRCm39)	D80E	probably damaging	Het
Gspt1	C	A	16: 11,071,843 (GRCm39)	G7C	unknown	Het
Hells	G	A	19: 38,943,244 (GRCm39)	S516N	probably benign	Het
Ints1	A	G	5: 139,738,542 (GRCm39)	S2069P	possibly damaging	Het
Kank4	G	A	4: 98,663,118 (GRCm39)	T690M	probably damaging	Het
Kcnq4	T	C	4: 120,573,006 (GRCm39)	N265S	possibly damaging	Het
Kif5b	C	A	18: 6,220,954 (GRCm39)	A385S	probably benign	Het
Map2	T	C	1: 66,454,415 (GRCm39)	S1102P	probably benign	Het
Mcm7	A	G	5: 138,163,133 (GRCm39)	S340P	possibly damaging	Het
Mcrs1	C	T	15: 99,144,876 (GRCm39)	R246H	possibly damaging	Het
Myo16	T	A	8: 10,610,226 (GRCm39)	M1189K	probably benign	Het
Or4d2	A	T	11: 87,783,892 (GRCm39)	I286N	probably damaging	Het
Or4k52	G	T	2: 111,610,804 (GRCm39)	M46I	probably benign	Het
Or7g29	G	A	9: 19,287,063 (GRCm39)	T38I	probably damaging	Het
Otog	A	G	7: 45,923,995 (GRCm39)	N1118S	probably damaging	Het
Pakap	T	C	4: 57,855,987 (GRCm39)	Y439H	probably damaging	Het
Pcdhb7	G	T	18: 37,474,846 (GRCm39)		probably benign	Het
Picalm	C	T	7: 89,819,806 (GRCm39)	T189I	possibly damaging	Het
Ptx4	T	A	17: 25,343,760 (GRCm39)	S337T	possibly damaging	Het
Rad51ap2	C	T	12: 11,508,313 (GRCm39)	S745L	probably benign	Het
Rspry1	G	A	8: 95,363,388 (GRCm39)		probably null	Het
Scn5a	T	G	9: 119,324,779 (GRCm39)	I1350L	probably damaging	Het
Sgk2	T	C	2: 162,839,755 (GRCm39)	L121P	probably damaging	Het
Slc17a1	A	T	13: 24,056,575 (GRCm39)		probably benign	Het
Slc6a12	A	G	6: 121,331,298 (GRCm39)	N183S	probably benign	Het
Spred1	G	A	2: 117,008,195 (GRCm39)	S367N	probably damaging	Het
Srpra	T	C	9: 35,122,646 (GRCm39)	V21A	probably benign	Het
Taar2	A	T	10: 23,816,627 (GRCm39)	I56F	possibly damaging	Het
Taf1a	T	G	1: 183,177,323 (GRCm39)	L67R	probably damaging	Het
Tbc1d10b	C	A	7: 126,797,779 (GRCm39)	R787S	possibly damaging	Het
Topbp1	T	A	9: 103,213,313 (GRCm39)	N1044K	probably benign	Het
Usp24	A	G	4: 106,232,871 (GRCm39)	T886A	probably benign	Het
Vmn2r26	A	G	6: 124,027,676 (GRCm39)	D472G	probably damaging	Het
Zyg11a	T	C	4: 108,061,943 (GRCm39)	N286S	possibly damaging	Het

Other mutations in Smg9

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01100:Smg9	APN	7	24,116,376 (GRCm39)	missense	probably damaging	1.00
IGL01432:Smg9	APN	7	24,120,691 (GRCm39)	critical splice donor site	probably null
IGL01869:Smg9	APN	7	24,115,949 (GRCm39)	missense	probably damaging	1.00
IGL02376:Smg9	APN	7	24,114,455 (GRCm39)	missense	probably benign	0.01
IGL03175:Smg9	APN	7	24,121,730 (GRCm39)	missense	probably damaging	1.00
IGL03204:Smg9	APN	7	24,120,337 (GRCm39)	missense	probably benign	0.02
R0318:Smg9	UTSW	7	24,120,313 (GRCm39)	missense	possibly damaging	0.80
R0578:Smg9	UTSW	7	24,114,468 (GRCm39)	missense	probably damaging	1.00
R0786:Smg9	UTSW	7	24,120,289 (GRCm39)	missense	probably benign	0.03
R2043:Smg9	UTSW	7	24,105,001 (GRCm39)	missense	possibly damaging	0.92
R2355:Smg9	UTSW	7	24,119,546 (GRCm39)	critical splice donor site	probably null
R3033:Smg9	UTSW	7	24,115,949 (GRCm39)	missense	probably damaging	1.00
R4091:Smg9	UTSW	7	24,120,292 (GRCm39)	missense	probably null	0.01
R4773:Smg9	UTSW	7	24,107,019 (GRCm39)	missense	possibly damaging	0.84
R5023:Smg9	UTSW	7	24,105,297 (GRCm39)	missense	possibly damaging	0.94
R6320:Smg9	UTSW	7	24,120,286 (GRCm39)	missense	probably benign
R6394:Smg9	UTSW	7	24,121,732 (GRCm39)	missense	probably damaging	1.00
R7156:Smg9	UTSW	7	24,120,286 (GRCm39)	missense	probably benign
R7269:Smg9	UTSW	7	24,105,495 (GRCm39)	missense	possibly damaging	0.88
R7311:Smg9	UTSW	7	24,120,058 (GRCm39)	missense	probably benign	0.14
R8972:Smg9	UTSW	7	24,120,055 (GRCm39)	missense	probably benign	0.04
R9323:Smg9	UTSW	7	24,114,465 (GRCm39)	missense	probably damaging	1.00
R9589:Smg9	UTSW	7	24,120,246 (GRCm39)	missense	probably damaging	1.00
R9707:Smg9	UTSW	7	24,102,869 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GCTGGACCTAATGTACCCATG -3'
(R):5'- CCAAAGTCATGCTGCTCAGAG -3'

Sequencing Primer
(F):5'- CATGGGGTGGAGTAAGGTTG -3'
(R):5'- ATGCTGCTCAGAGATCCTTCAGG -3'

Posted On

2016-10-05